Sequencing and de novo assembly of the Koshihikari genome and identification of the genomic region related to the eating quality of cooked rice

Development and application of indica–japonica SNP assays using the Fluidigm platform for rice genetic analysis and molecular breeding

(2020) Jeonghwan Seo et al.   MOLECULAR BREEDING

De novo Genome Assembly of the indica Rice Variety IR64 Using Linked-Read Sequencing and Nanopore Sequencing

(2020) Tsuyoshi Tanaka et al.   G3-Genes Genomes Genetics

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Koshihikari: a premium short-grain rice cultivar – its expansion and breeding in Japan

(2018) Asako Kobayashi et al.   Rice

Novel sequences, structural variations and gene presence variations of Asian cultivated rice

(2018) Zhiqiang Hu et al.   Scientific Data

Genomic variation in 3,010 diverse accessions of Asian cultivated rice

(2018) Wensheng Wang et al.   NATURE

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Efficiency of PacBio long read correction by 2nd generation Illumina sequencing

(2017) Medhat Mahmoud et al.   GENOMICS

New technologies boost genome quality

(2017) Elizabeth Pennisi   SCIENCE

Progress, challenges and the future of crop genomes

(2015) Todd P Michael et al.   CURRENT OPINION IN PLANT BIOLOGY

Reconstructing complex regions of genomes using long-read sequencing technology

(2014) J. Huddleston et al.   GENOME RESEARCH

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

The 3,000 rice genomes project: new opportunities and challenges for future rice research

(2014) Jia-Yang Li et al.   GigaScience

Rice Annotation Project Database (RAP-DB): An Integrative and Interactive Database for Rice Genomics

(2013) Hiroaki Sakai et al.   PLANT AND CELL PHYSIOLOGY

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Natural Variation in Hd17, a Homolog of Arabidopsis ELF3 That is Involved in Rice Photoperiodic Flowering

(2012) Kazuki Matsubara et al.   PLANT AND CELL PHYSIOLOGY

ALK, The Key Gene for Gelatinization Temperature, is a Modifier Gene for Gel Consistency in Rice (Oryza sativa L.)

(2011) Zhenyu Gao et al.   Journal of Integrative Plant Biology

Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms

(2010) Toshio Yamamoto et al.   BMC GENOMICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Detection of quantitative trait loci controlling pre-harvest sprouting resistance by using backcrossed populations of japonica rice cultivars

(2010) Kiyosumi Hori et al.   THEORETICAL AND APPLIED GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

PCR Marker-Based Evaluation of the Eating Quality ofJaponicaRice (Oryza sativa L.)

(2009) Puji Lestari et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

Mapping of QTLs for eating quality and physicochemical properties of the japonica rice ‘Koshihikari’

(2008) Takuya Wada et al.   BREEDING SCIENCE

Major QTLs for eating quality of an elite Japanese rice cultivar, Koshihikari, on the short arm of chromosome 3

(2008) Yoshinobu Takeuchi et al.   BREEDING SCIENCE